[Biopython-dev] Bio/cMarkovModelmodule.c

Peter biopython at maubp.freeserve.co.uk
Sat Oct 30 10:47:46 UTC 2010

On Sat, Oct 30, 2010 at 5:13 AM, Michiel de Hoon wrote:
> Hi everybody,
> I was looking at our C modules to see if they can be made
> ready for Python 3. I noticed that Bio/cMarkovModelmodule.c
> currently contains only one function, _logadd, which is used
> to speed up Bio.MarkovModel. Numpy 1.3 and later contain
> a function (logaddexp) that does exactly the same as _logadd.
> Since Bio.MarkovModel itself already uses Numpy, I think
> we can remove Bio/cMarkovModelmodule.c.

Sounds good :)

> For this to work, we either need to require Numpy >= 1.3
> in setup.py, or check for logaddexp when importing numpy
> in Bio.MarkovModel. I think requiring Numpy >= 1.3 in
> setup.py is better in the long run, so I would prefer that.
> Any other opinions?

The setup.py check sounds best.

We should check Numpy >= 1.3 is will be available for
Python 2.4 - this is relevant for Biopython 1.56 which
will still support Python 2.4

The most recent NumPy for Windows installer
for Python 2.4 was NumPy 1.2.1, but most Windows
users able to install Biopython via our Windows
installer would also be able to install a more recent
Python and NumPy - so not a big issue.

According to the old INSTALL.txt in Nump's github
repository it says that for numpy 1.3.0 they still
supported Python 2.4.


If there is any doubt about getting NumPy 1.3.x on
Python 2.4, we could postpone this change until
after we do the Biopython 1.56 release (probably in
November 2010) and drop support for Python 2.4.


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